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Frequently Asked Questions:

Table of contents

What is an OME-TIFF?

OME-TIFF is a TIFF images file format that contains a OME-XML metadata block.

For more documentation on the format, check out the OME webpage.

Is there additional requirements for my OME-TIFF?

  • OME-TIFF image channels must be unsigned 16-bit integers or unsigned 8-bit integers

    Images outputed by the mcmicro pipeline are unsigned 16-bit integers.

  • Cell segmentation masks must be unsigned 32-bit integers, loaded from a separate OME-TIFF

I see links on cell type and marker names in some Minerva Stories, how can I add it to my story?

Minerva has a built-in list of external links associated with commonly-encountered cell types and markers that can automatically be added to your story. The list is defined in main.js.

To enable the links, head to the index.html file generated by Minerva Author (an example of it can be found here), and remove the cellTypeData: [] and markerData: [] lines to enable automatically generated links to common cell types and cell markers.

Alternatively, provide your own list in the same file by using this format:

markerData: [
{"String":"name 1","Link":"url/1"},
{"String":"name 2","Link":"url/2"}
cellTypeData: [
{"String":"name 3","Link":"url/3"},
{"String":"name 4","Link":"url/4"}

The linked cell types and marker names will look like the ones in this story.

I’m seeing a message about missing image file when I start with a .story.json file. Why does this happen and what do I do?

The path to your image is written in the .story.json file when you save or export a Minerva Story. When you open a story file, if Minerva cannot find the image using the path in the file it will prompt you to provide a new path. An example of this is shown in the image below.

When this happens, first make sure that the image is on your device or in a mounted drive. You cannot use an online image for this. Then, all you need to do is navigate to the image on your device.

Minerva Author prompts "Missing 'LUNG-3-PR_40X.ome.tif'. Please find the image file location". Below the prompt, user is presented with a file browser for local drives.

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